2-44420692-A-G

Variant names:

• chr2-44420692-A-G
• rs17498753
• NM_024766.5:c.376+30387A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024766.5(CAMKMT):​c.376+30387A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,106 control chromosomes in the GnomAD database, including 1,670 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1670 hom., cov: 32)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401
• Publications: 4 publications found

Genes affected

CAMKMT (HGNC:26276): (calmodulin-lysine N-methyltransferase) This gene encodes a class I protein methyltransferase that acts in the formation of trimethyllysine in calmodulin. The protein contains a AdoMet-binding motif and may play a role in calcium-dependent signaling. [provided by RefSeq, Sep 2012]

LOC124907759 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024766.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMKMT	NM_024766.5	MANE Select	c.376+30387A>G		intron	N/A	NP_079042.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMKMT	ENST00000378494.8	TSL:1 MANE Select	c.376+30387A>G		intron	N/A	ENSP00000367755.3
	CAMKMT	ENST00000403853.7	TSL:1	c.376+30387A>G		intron	N/A	ENSP00000385124.3
	CAMKMT	ENST00000402247.5	TSL:2	c.376+30387A>G		intron	N/A	ENSP00000385587.1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19322 AN: 151988 Hom.: 1668 Cov.: 32

Gnomad AFR AF: 0.0314

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0396

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.141

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.127 AC: 19331 AN: 152106 Hom.: 1670 Cov.: 32 AF XY: 0.130 AC XY: 9697 AN XY: 74380

African (AFR) AF: 0.0314 AC: 1303 AN: 41556

American (AMR) AF: 0.220 AC: 3356 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3470

East Asian (EAS) AF: 0.0399 AC: 207 AN: 5186

South Asian (SAS) AF: 0.239 AC: 1151 AN: 4814

European-Finnish (FIN) AF: 0.131 AC: 1383 AN: 10534

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10668 AN: 67968

Other (OTH) AF: 0.139 AC: 293 AN: 2108

Alfa AF: 0.147 Hom.: 1890

Bravo AF: 0.127

Asia WGS AF: 0.121 AC: 420 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.6
DANN	Benign	0.67
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17498753; hg19: chr2-44647831;